Force Field Comparison of GM1 in a DOPC Bilayer Validated with AFM and FRET Experiments

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388955%3A_____%2F19%3A00508974" target="_blank" >RIV/61388955:_____/19:00508974 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/00216224:14740/19:00107895

Výsledek na webu

<a href="http://hdl.handle.net/11104/0299797" target="_blank" >http://hdl.handle.net/11104/0299797</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1021/acs.jpcb.9b05095" target="_blank" >10.1021/acs.jpcb.9b05095</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Force Field Comparison of GM1 in a DOPC Bilayer Validated with AFM and FRET Experiments

Popis výsledku v původním jazyce

The great physiological relevance of glycolipids is being increasingly recognized, and glycolipid interactions have been shown to be central to cell-cell recognition, neuronal plasticity, protein-ligand recognition, and other important processes. However, detailed molecular-level understanding of these processes remains to be fully resolved. Molecular dynamics simulations could reveal the details of the glycolipid interactions, but the results may be influenced by the choice of the employed force field. Here, we have compared the behavior and properties of GM1, a common, biologically important glycolipid, using the CHARMM36, OPLS, GROMOS, and Amber99-GLYCAMO6 (in bilayers comprising SLIPIDS and LIPID14 lipids) force fields in bilayers comprising 1,2-dioleoyl-snglycero-3-phosphocholine lipids and compared the results to atomic force microscopy and fluorescence resonance energy transfer experiments. We found discrepancies within the GM1 behavior displayed between the investigated force fields. Based on a direct comparison with complementary experimental results derived from fluorescence and AFM measurements, we recommend using the Amber99-GLYCAM force field in bilayers comprising LIPID14 or SLIPIDS lipids followed by CHARMM36 and OPLS force fields in simulations. The GROMOS force field is not recommended for reproducing the properties of the GM1 head group.

Název v anglickém jazyce

Force Field Comparison of GM1 in a DOPC Bilayer Validated with AFM and FRET Experiments

Popis výsledku anglicky

The great physiological relevance of glycolipids is being increasingly recognized, and glycolipid interactions have been shown to be central to cell-cell recognition, neuronal plasticity, protein-ligand recognition, and other important processes. However, detailed molecular-level understanding of these processes remains to be fully resolved. Molecular dynamics simulations could reveal the details of the glycolipid interactions, but the results may be influenced by the choice of the employed force field. Here, we have compared the behavior and properties of GM1, a common, biologically important glycolipid, using the CHARMM36, OPLS, GROMOS, and Amber99-GLYCAMO6 (in bilayers comprising SLIPIDS and LIPID14 lipids) force fields in bilayers comprising 1,2-dioleoyl-snglycero-3-phosphocholine lipids and compared the results to atomic force microscopy and fluorescence resonance energy transfer experiments. We found discrepancies within the GM1 behavior displayed between the investigated force fields. Based on a direct comparison with complementary experimental results derived from fluorescence and AFM measurements, we recommend using the Amber99-GLYCAM force field in bilayers comprising LIPID14 or SLIPIDS lipids followed by CHARMM36 and OPLS force fields in simulations. The GROMOS force field is not recommended for reproducing the properties of the GM1 head group.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10403 - Physical chemistry

Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2019

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Journal of Physical Chemistry B

ISSN

1520-6106

e-ISSN

—

Svazek periodika

123

Číslo periodika v rámci svazku

35

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

14

Strana od-do

7504-7517

Kód UT WoS článku

000484882800003

EID výsledku v databázi Scopus

2-s2.0-85072335907